We have shown that a recombination protein directly affects gene expression. The E. coli integration host factor alters the action of RNA polymerase, apparently by affecting its tendency to terminate elongation of RNA. This protein, together with a viral recombination protein, organize DNA into a wrapped structure prior to recombination. Studies of the topology of DNA recombinant products indicate the handedness of this wrapping is unique and resembles that found in chromatin. Alterations of the chemistry of recombining sites has been achieved; the semisynthetic DNA substrates for recombination are specifically blocked in breakage and reunion.